Aurica is a a 3rd generation Reyvateil. Because of her birth circumstances, she is classified as a Class-D Reyvateil, the lowest rank. Before the present time in the game, her home, Skuwat Village, was inflitrated by the Tenba Conglomorate. The Teru Tribe attacked Tenba while they were camped in Skuwat Village and the ensuing battle destroyed the town. Her parents went missing during the raid and she was later told that they died. However, she did not see their bodies firsthand, causing her serious mental trauma. Afterwards, she joins the Church of Elemia to work as a Reyvateil, in hopes of becoming one of the Holy Maidens. She appears inferior and gloomy at first but is getting more cheerful after met with Lyner. She is close friends with Claire, a singer in Nemo who also her childhood friend. She has a very strange way of cooking, though the food she makes always ends up tasting really good, while being almost obscene in appearance. Her dream is to open a music box shop.

Misha is a β pure-blood Reyvateil, also known to the Teru Tribe as the Hoshiyomi or Star Singer Her main purpose in life is to sing the song Chronicle Key to suppress Mir. She has been friends with Lyner since their childhood in Platina. He doesn't remember about her at first, though. She is also a good cook. She seems dispassionate, composed, but sometimes childish. Misha is quite bold and doesn't hesistate to make moves on Lyner. She suffers from acrophobia, and is also quite a klutz. It's worth noting that, despite being older than Aurica, she is trapped in a 12-year old girl body until her Song is recovered. After that, she regains her true form.

Shurelia is the administrator of Platina and the leader of the Knights of Elemia. As her direct subordinate, Lyner both admires and respects her. Although it is well-known that she is a Reyvateil, and a very powerful one at that, the identity of her Reyvateil type is left as a mystery for most of the game. It is only revealed partway through Phase 3 that she is in fact a Reyvateil Origin and in terms of sheer power, is second only to Mir. Though, she looks cold at first, Shurelia is actually shy and quite clumsy (sometimes she trips and lands with her face while chanting spells). She has no sense of direction and often gets lost, even in her own tower. She has a great fondness for bunnies and their related stuff (from dolls to bunny-shaped food to the point of bombs and restoring items). Aurica had once mistaken her for a robot because of her Linkage costume. Tough, extremely serious and no-nonsense as her role demands, she reveals herself to be desperate in gaining some sort of freedom and have a more ordinary, enjoyable life. She is the creator of Grathmelding, and has a very vast knowledge about technology. Her true name is Eoria/Eolia.

A cheerful girl and childhood friend of Croix's. She works as a Dive Therapist in Rakshek and is extremely knowledgeable in all matters related to Diving and Dive Therapy. She has a strange taste of cooking. Despite her cheerful exterior, she harbors many secrets that even Croix has no knowledge of. Luca's true name was the adopted name of her sister Leyka (aka Cloche Leythal Pastalia) but changed her named to Luca to cover up her identity after her biological mother Arshe was killed as a result of a conspiracy by Chancellor Alfman.

The revered Holy Maiden for the Grand Bell organization that Croix works for. She seems haughty, bossy and uptight initially, and treats Croix poorly at first, but is actually quite weak willed and pessimistic. She learns to be true to herself and share her truest feelings as she travels with Croix and his companions. She likes fancy things and stuffed animals called Gergo. She is also fond of children and dotes on them. Her true name is Leyka (Reisha's true daughter). She called Luca 'sis' on the ending.

She calls herself Jacqli. She has the special ability to control viruses. She seems to dislike humans. She initially gets in the way of Croix and his party, but soon switches over and becomes their greatest ally. Her knowledge of the mechanics of the Towers is invaluable and greatly surprises Shun. She seems to have a witty and semi-sarcastic personality, and looks like she trusts Croix enough to let him Dive into her. Her actual identity is Mir, the main boss of the first game. She traveled to Metafalss with Spica, the Grathnode merchant from Firefly Alley, and the two often make references to Lyner and his friends.

Saki (サキ, Saki?), full name Saki_zx.Flayed Junction Model Zero (咲_zx.零種フレードジャンクション, Saki_zx.reishu fureedojankushon?) is the main heroine and a γ Sublimated Reyvateil who was created in Archia Laboratory for a project that would have a great impact on the world. She escaped before the project was executed and was on the run for several years before she met Aoto. When she's extremely emotionally strained, she can use a power known as Miracle. Her Mind Guardian is Bombastic Man.

Finnel (フィンネル, Finneru?), full name Finnel_ax.Forged Clustania (フィンネル_ax.鋳種クラスタニア, Finnel_ax.tetsushu kurasutania?), is another main heroine and a really clumsy β-type Reyvateil who works in a restaurant known as Yokkora Bistro as the mascot girl, which is situated on the Eternus Shaft. Her clumsiness makes people nervous with her reckless actions. As unlikely as it may seem, Soma, the deadliest hitman hides deep within her. She follows Tatsumi around because her duty is to bring the Heart of Gaea to the soil of Clustania. She's a typical tsundere who hates the fact that she's so stubborn. She is also secretly a masochist.
She loves cold treats like ice cream and snow cones, but because she's always so careless, she always gets brain freeze.

Tyria is the Third Origin Reyvateil, and Administrator of the Third Tower in Sol Cluste and the Tower itself. She is the true form of the goddess that Aurica used to worship in the first game, Melody of Elemia, and the different appearance is because no one in Sol Ciel had ever seen Tyria's true appearance; the images that appeared of her were all fabricated by the imagination of the Elemians. She is also the Reyvateils' master. She is a rare Reyvateil Origin. Her personality is very strange, by modern standards. She is very blatant and blunt. She likes food made from flour, such as breads and cakes.